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1VPS
Asym. Unit
Info
Asym.Unit (282 KB)
Biol.Unit 1 (275 KB)
Biol.Unit 2 (545 KB)
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(1)
Title
:
POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE
Authors
:
T. Stehle, S. C. Harrison
Date
:
07 Mar 97 (Deposition) - 15 May 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: A,B,C,D,E (2x)
Keywords
:
Virus Coat Protein, Oligosaccharide Binding, Virus Assembly, Sialic Acid, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Stehle, S. C. Harrison
High-Resolution Structure Of A Polyomavirus Vp1-Oligosaccharide Complex: Implications For Assembly And Receptor Binding.
Embo J. V. 16 5139 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
1e: BETA-D-GALACTOSE (GALe)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3a: O-SIALIC ACID (SIAa)
3b: O-SIALIC ACID (SIAb)
3c: O-SIALIC ACID (SIAc)
3d: O-SIALIC ACID (SIAd)
3e: O-SIALIC ACID (SIAe)
3f: O-SIALIC ACID (SIAf)
3g: O-SIALIC ACID (SIAg)
3h: O-SIALIC ACID (SIAh)
3i: O-SIALIC ACID (SIAi)
3j: O-SIALIC ACID (SIAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
5
Ligand/Ion
BETA-D-GALACTOSE
2
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SIA
10
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GAL A:2 , TYR A:72 , ARG A:77 , GLY A:78 , THR A:291 , ASN A:293 , HIS A:298 , HOH A:496 , HOH A:499 , HOH A:603 , HOH A:662 , HOH A:669 , HOH A:678 , ASP B:85
BINDING SITE FOR RESIDUE SIA A 1
02
AC2
SOFTWARE
SIA A:1 , NAG A:3 , GLY A:78 , ASN A:93 , THR A:94 , HOH A:660 , HOH A:662 , HOH A:663
BINDING SITE FOR RESIDUE GAL A 2
03
AC3
SOFTWARE
GAL A:2 , SIA A:4
BINDING SITE FOR RESIDUE NAG A 3
04
AC4
SOFTWARE
NAG A:3 , ASN A:80 , LEU A:81 , THR A:83 , SER A:89 , LYS A:186 , HOH A:400 , HOH A:414 , HOH A:698
BINDING SITE FOR RESIDUE SIA A 4
05
AC5
SOFTWARE
GAL B:2 , TYR B:72 , ARG B:77 , GLY B:78 , THR B:291 , ASN B:293 , HIS B:298 , HOH B:518 , HOH B:521 , HOH B:570 , HOH B:714 , HOH B:715 , HOH B:725 , ASP C:85
BINDING SITE FOR RESIDUE SIA B 1
06
AC6
SOFTWARE
SIA B:1 , NAG B:3 , GLY B:78 , ASN B:93 , THR B:94 , HOH B:659 , HOH B:684 , HOH B:713 , HOH B:714
BINDING SITE FOR RESIDUE GAL B 2
07
AC7
SOFTWARE
GAL B:2 , SIA B:4 , HOH B:713
BINDING SITE FOR RESIDUE NAG B 3
08
AC8
SOFTWARE
NAG B:3 , ASN B:80 , LEU B:81 , THR B:83 , SER B:89 , LYS B:186 , HOH B:434 , HOH B:711 , HOH B:712
BINDING SITE FOR RESIDUE SIA B 4
09
AC9
SOFTWARE
GAL C:2 , TYR C:72 , ARG C:77 , GLY C:78 , THR C:291 , ASN C:293 , HIS C:298 , HOH C:512 , HOH C:515 , HOH C:579 , HOH C:724 , HOH C:747 , HOH C:758 , ASP D:85
BINDING SITE FOR RESIDUE SIA C 1
10
BC1
SOFTWARE
SIA C:1 , NAG C:3 , GLY C:78 , ASN C:93 , THR C:94 , HOH C:598 , HOH C:626 , HOH C:724 , HOH C:726
BINDING SITE FOR RESIDUE GAL C 2
11
BC2
SOFTWARE
GAL C:2 , SIA C:4 , HOH C:598
BINDING SITE FOR RESIDUE NAG C 3
12
BC3
SOFTWARE
NAG C:3 , ASN C:80 , LEU C:81 , SER C:89 , HOH C:418 , HOH C:432 , HOH C:749
BINDING SITE FOR RESIDUE SIA C 4
13
BC4
SOFTWARE
GAL D:2 , TYR D:72 , ARG D:77 , GLY D:78 , THR D:291 , ASN D:293 , HIS D:298 , HOH D:523 , HOH D:526 , HOH D:634 , HOH D:719 , HOH D:720 , HOH D:735 , HOH D:742 , HOH D:749 , ASP E:85
BINDING SITE FOR RESIDUE SIA D 1
14
BC5
SOFTWARE
SIA D:1 , NAG D:3 , GLY D:78 , ASN D:93 , THR D:94 , HOH D:717 , HOH D:720 , HOH D:726
BINDING SITE FOR RESIDUE GAL D 2
15
BC6
SOFTWARE
TYR C:294 , GAL D:2 , SIA D:4 , HOH D:734 , HOH D:740
BINDING SITE FOR RESIDUE NAG D 3
16
BC7
SOFTWARE
ASN B:149 , HOH B:650 , TYR C:294 , NAG D:3 , ASN D:80 , LEU D:81 , THR D:83 , SER D:89 , LYS D:186 , HOH D:628 , HOH D:718 , HOH D:728
BINDING SITE FOR RESIDUE SIA D 4
17
BC8
SOFTWARE
ASP A:85 , GAL E:2 , TYR E:72 , ARG E:77 , GLY E:78 , THR E:291 , ASN E:293 , HIS E:298 , HOH E:528 , HOH E:531 , HOH E:595 , HOH E:668 , HOH E:672
BINDING SITE FOR RESIDUE SIA E 1
18
BC9
SOFTWARE
SIA E:1 , NAG E:3 , GLY E:78 , ASN E:93 , THR E:94 , HOH E:668 , HOH E:670
BINDING SITE FOR RESIDUE GAL E 2
19
CC1
SOFTWARE
GAL E:2 , SIA E:4 , HOH E:698
BINDING SITE FOR RESIDUE NAG E 3
20
CC2
SOFTWARE
NAG E:3 , ASN E:80 , LEU E:81 , THR E:83 , SER E:89 , HOH E:435 , HOH E:665
BINDING SITE FOR RESIDUE SIA E 4
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1vpsa_ (A:)
1b: SCOP_d1vpsb_ (B:)
1c: SCOP_d1vpsc_ (C:)
1d: SCOP_d1vpsd_ (D:)
1e: SCOP_d1vpse_ (E:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Group I dsDNA viruses
(30)
Family
:
Papovaviridae-like VP
(19)
Protein domain
:
Polyomavirus coat proteins
(6)
Murine polyomavirus, strain small-plaque 16 [TaxId: 10634]
(5)
1a
d1vpsa_
A:
1b
d1vpsb_
B:
1c
d1vpsc_
C:
1d
d1vpsd_
D:
1e
d1vpse_
E:
[
close SCOP info
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1vpsB00 (B:32-320)
1b: CATH_1vpsA00 (A:32-316)
1c: CATH_1vpsC00 (C:32-316)
1d: CATH_1vpsD00 (D:32-316)
1e: CATH_1vpsE00 (E:32-316)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Polyomavirus Vp1; Chain A
(9)
Homologous Superfamily
:
Polyomavirus Vp1, chain A
(8)
Murine polyomavirus. Organism_taxid: 10634.
(2)
1a
1vpsB00
B:32-320
1b
1vpsA00
A:32-316
1c
1vpsC00
C:32-316
1d
1vpsD00
D:32-316
1e
1vpsE00
E:32-316
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Polyoma_coat_1vpsE01 (E:32-316)
1b: PFAM_Polyoma_coat_1vpsE02 (E:32-316)
1c: PFAM_Polyoma_coat_1vpsE03 (E:32-316)
1d: PFAM_Polyoma_coat_1vpsE04 (E:32-316)
1e: PFAM_Polyoma_coat_1vpsE05 (E:32-316)
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Clans
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Organisms
(
)
(
)
Clan
:
no clan defined [family: Polyoma_coat]
(8)
Family
:
Polyoma_coat
(8)
Murine polyomavirus (strain P16 small-plaque) (MPyV)
(4)
1a
Polyoma_coat-1vpsE01
E:32-316
1b
Polyoma_coat-1vpsE02
E:32-316
1c
Polyoma_coat-1vpsE03
E:32-316
1d
Polyoma_coat-1vpsE04
E:32-316
1e
Polyoma_coat-1vpsE05
E:32-316
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